JAL-3626 from JAL-3253-applet Jalview.java

[jalview.git] / src / jalview / gui / Preferences.java

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 646bf61..de67768 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -20,29 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.bin.Cache;
-import jalview.gui.Help.HelpId;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.BackupFiles;
-import jalview.io.BackupFilesPresetEntry;
-import jalview.io.FileFormatI;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GPreferences;
-import jalview.jbgui.GSequenceLink;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemes;
-import jalview.schemes.ResidueColourScheme;
-import jalview.urls.UrlLinkTableModel;
-import jalview.urls.api.UrlProviderFactoryI;
-import jalview.urls.api.UrlProviderI;
-import jalview.urls.desktop.DesktopUrlProviderFactory;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.util.UrlConstants;
-import jalview.ws.sifts.SiftsSettings;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;
@@ -74,6 +51,28 @@ import javax.swing.table.TableModel;
 import javax.swing.table.TableRowSorter;
 
 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.gui.Help.HelpId;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.BackupFiles;
+import jalview.io.BackupFilesPresetEntry;
+import jalview.io.FileFormatI;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GPreferences;
+import jalview.jbgui.GSequenceLink;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
+import jalview.urls.UrlLinkTableModel;
+import jalview.urls.api.UrlProviderFactoryI;
+import jalview.urls.api.UrlProviderI;
+import jalview.urls.desktop.DesktopUrlProviderFactory;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.UrlConstants;
+import jalview.ws.sifts.SiftsSettings;
 
 /**
  * DOCUMENT ME!
@@ -833,7 +832,7 @@ public class Preferences extends GPreferences
     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
     if (menuLinks.isEmpty())
     {
-      Cache.removeNoSave("SEQUENCE_LINKS");
+      Cache.removePropertyNoSave("SEQUENCE_LINKS");
     }
     else
     {
@@ -844,7 +843,7 @@ public class Preferences extends GPreferences
     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
     if (nonMenuLinks.isEmpty())
     {
-      Cache.removeNoSave("STORED_LINKS");
+      Cache.removePropertyNoSave("STORED_LINKS");
     }
     else
     {
@@ -948,8 +947,7 @@ public class Preferences extends GPreferences
       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
-      Cache.applicationProperties
-              .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
+      Cache.setPropertyNoSave(BackupFilesPresetEntry.CUSTOMCONFIG,
                       customBFPE.toString());
     }
 
@@ -968,7 +966,43 @@ public class Preferences extends GPreferences
     }
   }
 
-  /**
+  public static void setAppletDefaults()
+  {
+
+    // http://www.jalview.org/old/v2_8/examples/appletParameters.html
+
+    // showConservation true or false Default is true.
+    // showQuality true or false Default is true.
+    // showConsensus true or false Default is true.
+    // showFeatureSettings true or false Shows the feature settings window when
+    // startin
+    // showTreeBootstraps true or false (default is true) show or hide branch
+    // bootstraps
+    // showTreeDistances true or false (default is true) show or hide branch
+    // lengths
+    // showUnlinkedTreeNodes true or false (default is false) indicate if
+    // unassociated nodes should be highlighted in the tree view
+    // showUnconserved true of false (default is false) When true, only gaps and
+    // symbols different to the consensus sequence ions of the alignment
+    // showGroupConsensus true of false (default is false) When true, shows
+    // consensus annotation row for any groups on the alignment. (since 2.7)
+    // showGroupConservation true of false (default is false) When true, shows
+    // amino-acid property conservation annotation row for any groups on the
+    // showConsensusHistogram true of false (default is true) When true, shows
+    // the percentage occurence of the consensus symbol for each column as a
+    // showSequenceLogo true of false (default is false) When true, shows a
+    // sequence logo above the consensus sequence (overlaid above the Consensus
+
+    Cache.setPropertyNoSave(SHOW_CONSERVATION, "true");
+    Cache.setPropertyNoSave(SHOW_QUALITY, "false");
+    Cache.setPropertyNoSave(SHOW_CONSENSUS, "true");
+    Cache.setPropertyNoSave(SHOW_UNCONSERVED, "false");
+    Cache.setPropertyNoSave(SHOW_GROUP_CONSERVATION, "false");
+    Cache.setPropertyNoSave(SHOW_GROUP_CONSENSUS, "false");
+
+    // TODO -- just a start here
+  }
+ /**
    * Do any necessary validation before saving settings. Return focus to the
    * first tab which fails validation.
    *